ETNK1

ethanolamine kinase 1

Basic information

Region (hg38): 12:22625075-22690665

Links

ENSG00000139163

∙ NCBI:55500 ∙ OMIM:609858 ∙ HGNC:24649 ∙ Uniprot:Q9HBU6 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ETNK1 gene.

not_specified (30 variants)
Teratoma (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ETNK1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000018638.5. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			29 clinvar			29
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	29	0	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ETNK1	protein_coding	protein_coding	ENST00000266517	8	65591

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.926	0.0744	125725	0	23	125748	0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.91	161	245	0.656	0.0000115	2930
Missense in Polyphen		30	88.175	0.34023		1123
Synonymous	-0.0325	95	94.6	1.00	0.00000438	875
Loss of Function	3.70	3	21.5	0.139	0.00000105	242

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000444	0.000428
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000551	0.0000462
European (Non-Finnish)	0.0000490	0.0000439
Middle Eastern	0.00	0.00
South Asian	0.000131	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Highly specific for ethanolamine phosphorylation. May be a rate-controlling step in phosphatidylethanolamine biosynthesis.;
Pathway: Glycerophospholipid metabolism - Homo sapiens (human);Kennedy pathway from Sphingolipids;One carbon metabolism and related pathways;Metabolism of lipids;Metabolism;Synthesis of PE;phosphatidylethanolamine biosynthesis II;Glycerophospholipid biosynthesis;Phospholipid metabolism (Consensus)

Recessive Scores

pRec: 0.107

Intolerance Scores

loftool: 0.292
rvis_EVS: 0.04
rvis_percentile_EVS: 56.92

Haploinsufficiency Scores

pHI: 0.164
hipred: Y
hipred_score: 0.648
ghis: 0.604

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: K
gene_indispensability_pred: E
gene_indispensability_score: 0.992

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

Gene name: Etnk1
Phenotype: immune system phenotype; hematopoietic system phenotype;

Gene ontology

Biological process: phosphatidylethanolamine biosynthetic process;phosphorylation
Cellular component: nucleoplasm;cytosol;plasma membrane;membrane
Molecular function: ethanolamine kinase activity;protein binding;ATP binding